def xoppy_calc_mlayer(self):
# copy the variable locally, so no more use of self.
MODE = self.MODE
SCAN = self.SCAN
F12_FLAG = self.F12_FLAG
SUBSTRATE = self.SUBSTRATE
ODD_MATERIAL = self.ODD_MATERIAL
EVEN_MATERIAL = self.EVEN_MATERIAL
ENERGY = self.ENERGY
THETA = self.THETA
SCAN_STEP = self.SCAN_STEP
NPOINTS = self.NPOINTS
ODD_THICKNESS = self.ODD_THICKNESS
EVEN_THICKNESS = self.EVEN_THICKNESS
NLAYERS = self.NLAYERS
FILE = self.FILE
for file in ["mlayer.inp", "mlayer.par", "mlayer.f12"]:
try:
os.remove(os.path.join(locations.home_bin_run(), file))
except:
pass
#
# write input file for Fortran mlayer: mlayer.inp
#
f = open('mlayer.inp', 'w')
if SCAN == 0 and MODE == 0: a0 = 1
if SCAN == 1 and MODE == 0: a0 = 2
if SCAN == 0 and MODE == 1: a0 = 3
if SCAN == 1 and MODE == 1: a0 = 4
f.write("%d \n" % a0)
f.write("N\n")
f.write("%g\n" % (codata.h * codata.c / codata.e * 1e10 / ENERGY))
f.write("%g\n" % THETA)
#
if SCAN == 0:
f.write("%g\n" % SCAN_STEP)
a2 = codata.h * codata.c / codata.e * 1e10 / ENERGY
a3 = codata.h * codata.c / codata.e * 1e10 / (ENERGY + SCAN_STEP)
a4 = a3 - a2
if SCAN != 0:
f.write("%g\n" % a4)
#
f.write("%d\n" % NPOINTS)
if MODE == 0:
f.write("%d\n" % NLAYERS)
if MODE == 0:
if a0 != 5:
f.write("%g %g \n" % (ODD_THICKNESS, EVEN_THICKNESS))
else:
for i in range(NLAYERS):
f.write("%g %g \n" % (ODD_THICKNESS, EVEN_THICKNESS))
if MODE != 0:
f1 = open(FILE, 'r')
a5 = f1.read()
f1.close()
if MODE != 0:
print("Number of layers in %s file is %d " % (FILE, NLAYERS))
f.write("%d\n" % NLAYERS)
f.write(a5)
f.write("mlayer.par\n")
f.write("mlayer.dat\n")
f.write("6\n")
f.close()
print('File written to disk: mlayer.inp')
#
# create f12 file
#
if F12_FLAG == 0:
energy = numpy.arange(0, 500)
elefactor = numpy.log10(10000.0 / 30.0) / 300.0
energy = 10.0 * 10**(energy * elefactor)
f12_s = f1f2_calc(SUBSTRATE, energy)
f12_e = f1f2_calc(EVEN_MATERIAL, energy)
f12_o = f1f2_calc(ODD_MATERIAL, energy)
f = open("mlayer.f12", 'w')
f.write(
'; File created by xoppy for materials [substrate=%s,even=%s,odd=%s]: \n'
% (SUBSTRATE, EVEN_MATERIAL, ODD_MATERIAL))
f.write('; Atomic masses: \n')
f.write(
"%g %g %g \n" %
(xraylib.AtomicWeight(xraylib.SymbolToAtomicNumber(SUBSTRATE)),
xraylib.AtomicWeight(
xraylib.SymbolToAtomicNumber(EVEN_MATERIAL)),
xraylib.AtomicWeight(
xraylib.SymbolToAtomicNumber(ODD_MATERIAL))))
f.write('; Densities: \n')
f.write("%g %g %g \n" %
(xraylib.ElementDensity(
xraylib.SymbolToAtomicNumber(SUBSTRATE)),
xraylib.ElementDensity(
xraylib.SymbolToAtomicNumber(EVEN_MATERIAL)),
xraylib.ElementDensity(
xraylib.SymbolToAtomicNumber(ODD_MATERIAL))))
f.write('; Number of energy points: \n')
f.write("%d\n" % (energy.size))
f.write(
'; For each energy point, energy[eV], f1[substrate], f2[substrate], f1[even], f2[even], f1[odd], f2[odd]: \n'
)
for i in range(energy.size):
f.write("%g %g %g %g %g %g %g \n" %
(energy[i], f12_s[0, i], f12_s[1, i], f12_e[0, i],
f12_e[1, i], f12_o[0, i], f12_o[1, i]))
f.close()
print('File written to disk: mlayer.f12')
#
# run external program mlayer
#
if platform.system() == "Windows":
command = os.path.join(locations.home_bin(),
'mlayer.exe < mlayer.inp')
else:
command = "'" + os.path.join(locations.home_bin(),
'mlayer') + "' < mlayer.inp"
print("Running command '%s' in directory: %s " %
(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
#send exchange
calculated_data = DataExchangeObject(
"XOPPY", self.get_data_exchange_widget_name())
try:
if SCAN == 0:
calculated_data.add_content("xoppy_data",
numpy.loadtxt("mlayer.dat"))
calculated_data.add_content("plot_x_col", 0)
calculated_data.add_content("plot_y_col", 3)
elif SCAN == 1: # internal scan is in wavelength. Add a column with energy
aa = numpy.loadtxt("mlayer.dat")
photon_energy = (codata.h * codata.c / codata.e * 1e10) / aa[:,
0]
bb = numpy.zeros((aa.shape[0], 1 + aa.shape[1]))
bb[:, 0] = photon_energy
bb[:, 1:] = aa
calculated_data.add_content("xoppy_data", bb)
calculated_data.add_content("plot_x_col", 0)
calculated_data.add_content("plot_y_col", 4)
calculated_data.add_content("units_to_degrees", 1.0)
except:
pass
try:
info = "ML %s(%3.2f A):%s(%3.2f A) %d pairs; E=%5.3f eV" % (
ODD_MATERIAL, ODD_THICKNESS, EVEN_MATERIAL, EVEN_THICKNESS,
NLAYERS, ENERGY)
calculated_data.add_content("info", info)
except:
pass
return calculated_data
def xoppy_calc_xf1f2(self):
MAT_FLAG = self.MAT_FLAG
DESCRIPTOR = self.DESCRIPTOR
density = self.DENSITY
CALCULATE = self.CALCULATE
GRID = self.GRID
GRIDSTART = self.GRIDSTART
GRIDEND = self.GRIDEND
GRIDN = self.GRIDN
THETAGRID = self.THETAGRID
ROUGH = self.ROUGH
THETA1 = self.THETA1
THETA2 = self.THETA2
THETAN = self.THETAN
if MAT_FLAG == 0: # element
descriptor = DESCRIPTOR
density = xraylib.ElementDensity(
xraylib.SymbolToAtomicNumber(DESCRIPTOR))
elif MAT_FLAG == 1: # formula
descriptor = DESCRIPTOR
if GRID == 0: # standard energy grid
energy = numpy.arange(0, 500)
elefactor = numpy.log10(10000.0 / 30.0) / 300.0
energy = 10.0 * 10**(energy * elefactor)
elif GRID == 1: # user energy grid
if GRIDN == 1:
energy = numpy.array([GRIDSTART])
else:
energy = numpy.linspace(GRIDSTART, GRIDEND, GRIDN)
elif GRID == 2: # single energy point
energy = numpy.array([GRIDSTART])
if THETAGRID == 0:
theta = numpy.array([THETA1])
else:
theta = numpy.linspace(THETA1, THETA2, THETAN)
CALCULATE_items = [
'f1', 'f2', 'delta', 'beta', 'mu [cm^-1]', 'mu [cm^2/g]',
'Cross Section [barn]', 'reflectivity-s', 'reflectivity-p',
'reflectivity-unpol', 'delta/beta '
]
out = numpy.zeros((energy.size, theta.size))
for i, itheta in enumerate(theta):
if MAT_FLAG == 0: # element
tmp = f1f2_calc(descriptor,
energy,
1e-3 * itheta,
F=1 + CALCULATE,
rough=ROUGH,
density=density)
out[:, i] = tmp
else:
tmp = f1f2_calc_mix(descriptor,
energy,
1e-3 * itheta,
F=1 + CALCULATE,
rough=ROUGH,
density=density)
out[:, i] = tmp
if ((energy.size == 1) and (theta.size == 1)):
info = "** Single value calculation E=%g eV, theta=%g mrad, Result(F=%d)=%g " % (
energy[0], theta[0], 1 + CALCULATE, out[0, 0])
labels = ["Energy [eV]", CALCULATE_items[CALCULATE]]
tmp = numpy.vstack((energy, out[:, 0]))
print(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>", energy.shape, out.shape,
tmp.shape)
out_dict = {
"application": "xoppy",
"name": "xf12",
"info": info,
"data": tmp,
"labels": labels
}
elif theta.size == 1:
tmp = numpy.vstack((energy, out[:, 0]))
labels = ["Energy [eV]", CALCULATE_items[CALCULATE]]
out_dict = {
"application": "xoppy",
"name": "xf12",
"data": tmp,
"labels": labels
}
elif energy.size == 1:
tmp = numpy.vstack((theta, out[0, :]))
labels = ["Theta [mrad]", CALCULATE_items[CALCULATE]]
out_dict = {
"application": "xoppy",
"name": "xf12",
"data": tmp,
"labels": labels
}
else:
labels = [r"energy[eV]", r"theta [mrad]"]
out_dict = {
"application": "xoppy",
"name": "xf12",
"data2D": out,
"dataX": energy,
"dataY": theta,
"labels": labels
}
#
#
#
if "info" in out_dict.keys():
print(out_dict["info"])
#send exchange
calculated_data = DataExchangeObject(
"XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", out_dict["data"].T)
calculated_data.add_content("plot_x_col", 0)
calculated_data.add_content("plot_y_col", -1)
except:
pass
try:
calculated_data.add_content("labels", out_dict["labels"])
except:
pass
try:
calculated_data.add_content("info", out_dict["info"])
except:
pass
try:
calculated_data.add_content("data2D", out_dict["data2D"])
calculated_data.add_content("dataX", out_dict["dataX"])
calculated_data.add_content("dataY", out_dict["dataY"])
except:
pass
if self.DUMP_TO_FILE:
with open(self.FILE_NAME, "w") as file:
try:
file.write("#F %s\n" % self.FILE_NAME)
file.write("\n#S 1 xoppy f1f2 results\n")
print("data shape", out_dict["data"].shape)
print("labels: ", out_dict["labels"])
file.write("#N 2\n")
file.write("#L %s %s\n" %
(out_dict["labels"][0], out_dict["labels"][1]))
out = out_dict["data"]
for j in range(out.shape[1]):
file.write(
("%19.12e " * out.shape[0] + "\n") %
tuple(out[i, j] for i in range(out.shape[0])))
file.close()
print("File written to disk: %s \n" % self.FILE_NAME)
except:
raise Exception(
"CrossSec: The data could not be dumped onto the specified file!\n"
)
return calculated_data
file_name = oasysgui.selectFileFromDialog(None, None, "Open ASC file")
congruence.checkFile(file_name)
data = numpy.loadtxt(file_name, skiprows=1)
energies = data[:, 0]
angles = numpy.radians((180 - data[:, 3]) / 2)
reflectivities = numpy.zeros((energies.size, angles.size))
density = xraylib.ElementDensity(xraylib.SymbolToAtomicNumber("Au"))
for i, itheta in enumerate(angles):
reflectivities[:, i] = f1f2_calc("Au",
energies,
itheta,
F=10,
rough=0.0,
density=density)
angles = numpy.degrees(angles)
file_out = open(os.path.dirname(file_name) + "/reflectivities.out",
mode="w")
rows = ["Energy (eV) Theta (deg) Reflectivity\n"]
for i in range(0, energies.size):
for j in range(0, angles.size):
rows.append(
str(energies[i]) + " " + str(angles[j]) + " " +
str(reflectivities[i, j]) + "\n")
file_out.writelines(rows)
def xoppy_calc_mlayer(self):
# copy the variable locally, so no more use of self.
MODE = self.MODE
SCAN = self.SCAN
F12_FLAG = self.F12_FLAG
SUBSTRATE = self.SUBSTRATE
ODD_MATERIAL = self.ODD_MATERIAL
EVEN_MATERIAL = self.EVEN_MATERIAL
ENERGY = self.ENERGY
THETA = self.THETA
SCAN_STEP = self.SCAN_STEP
NPOINTS = self.NPOINTS
ODD_THICKNESS = self.ODD_THICKNESS
EVEN_THICKNESS = self.EVEN_THICKNESS
NLAYERS = self.NLAYERS
FILE=self.FILE
for file in ["mlayer.inp","mlayer.par","mlayer.f12"]:
try:
os.remove(os.path.join(locations.home_bin_run(),file))
except:
pass
#
# write input file for Fortran mlayer: mlayer.inp
#
f = open('mlayer.inp','w')
if SCAN == 0 and MODE == 0: a0 = 1
if SCAN == 1 and MODE == 0: a0 = 5
if SCAN == 0 and MODE == 1: a0 = 3
if SCAN == 1 and MODE == 1: a0 = 5
f.write("%d \n"%a0)
f.write("N\n")
f.write("%g\n"%( codata.h * codata.c / codata.e * 1e10 / ENERGY))
f.write("%g\n"%THETA)
if SCAN == 0:
f.write("%g\n"%SCAN_STEP)
a2 = codata.h * codata.c / codata.e * 1e10 / ENERGY
a3 = codata.h * codata.c / codata.e * 1e10 / (ENERGY + SCAN_STEP)
a4 = a3 - a2
if SCAN != 0:
f.write("%g\n"%a4)
f.write("%d\n"%NPOINTS)
if MODE == 0:
f.write("%d\n"%NLAYERS)
if MODE == 0:
if a0 != 5:
f.write("%g %g \n"%(ODD_THICKNESS,EVEN_THICKNESS))
else:
for i in range(NLAYERS):
f.write("%g %g \n"%(ODD_THICKNESS,EVEN_THICKNESS))
if MODE != 0:
f1 = open(FILE,'r')
a5 = f1.read()
f1.close()
if MODE != 0:
print("Number of layers in %s file is %d "%(FILE,NLAYERS))
f.write("%d\n"%NLAYERS)
f.write(a5)
f.write("mlayer.par\n")
f.write("mlayer.dat\n")
f.write("6\n")
f.close()
print('File written to disk: mlayer.inp')
#
# create f12 file
#
if F12_FLAG == 0:
energy = numpy.arange(0,500)
elefactor = numpy.log10(10000.0 / 30.0) / 300.0
energy = 10.0 * 10**(energy * elefactor)
f12_s = f1f2_calc(SUBSTRATE,energy)
f12_e = f1f2_calc(EVEN_MATERIAL,energy)
f12_o = f1f2_calc(ODD_MATERIAL,energy)
f = open("mlayer.f12",'w')
f.write('; File created by xoppy for materials [substrate=%s,even=%s,odd=%s]: \n'%(SUBSTRATE,EVEN_MATERIAL,ODD_MATERIAL))
f.write('; Atomic masses: \n')
f.write("%g %g %g \n"%(xraylib.AtomicWeight(xraylib.SymbolToAtomicNumber(SUBSTRATE)),
xraylib.AtomicWeight(xraylib.SymbolToAtomicNumber(EVEN_MATERIAL)),
xraylib.AtomicWeight(xraylib.SymbolToAtomicNumber(ODD_MATERIAL)) ))
f.write('; Densities: \n')
f.write("%g %g %g \n"%(xraylib.ElementDensity(xraylib.SymbolToAtomicNumber(SUBSTRATE)),
xraylib.ElementDensity(xraylib.SymbolToAtomicNumber(EVEN_MATERIAL)),
xraylib.ElementDensity(xraylib.SymbolToAtomicNumber(ODD_MATERIAL)) ))
f.write('; Number of energy points: \n')
f.write("%d\n"%(energy.size))
f.write('; For each energy point, energy[eV], f1[substrate], f2[substrate], f1[even], f2[even], f1[odd], f2[odd]: \n')
for i in range(energy.size):
f.write("%g %g %g %g %g %g %g \n"%(energy[i],f12_s[0,i],f12_s[1,i],f12_e[0,i],f12_e[1,i],f12_o[0,i],f12_o[1,i]))
f.close()
print('File written to disk: mlayer.f12')
#
# run external program mlayer
#
command = os.path.join(locations.home_bin(), 'mlayer') + " < mlayer.inp"
print("Running command '%s' in directory: %s "%(command, locations.home_bin_run()))
print("\n--------------------------------------------------------\n")
os.system(command)
print("\n--------------------------------------------------------\n")
#send exchange
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", numpy.loadtxt("mlayer.dat"))
calculated_data.add_content("plot_x_col", 0)
calculated_data.add_content("plot_y_col", 3)
calculated_data.add_content("units_to_degrees", 1.0)
except:
pass
try:
calculated_data.add_content("labels",["Grazing angle Theta [deg]","s-reflectivity","p-reflectivity","averaged reflectivity","s-phase shift","p-phase shift","(s-electric field)^2","(p-electric field)^2"])
except:
pass
try:
info = "ML %s(%3.2f A):%s(%3.2f A) %d pairs; E=%5.3f eV"%(ODD_MATERIAL,ODD_THICKNESS,EVEN_MATERIAL,EVEN_THICKNESS,NLAYERS,ENERGY)
calculated_data.add_content("info",info)
except:
pass
return calculated_data
def xoppy_calc_xf1f2(self):
MAT_FLAG = self.MAT_FLAG
DESCRIPTOR = self.DESCRIPTOR
density = self.DENSITY
CALCULATE = self.CALCULATE
GRID = self.GRID
GRIDSTART = self.GRIDSTART
GRIDEND = self.GRIDEND
GRIDN = self.GRIDN
THETAGRID = self.THETAGRID
ROUGH = self.ROUGH
THETA1 = self.THETA1
THETA2 = self.THETA2
THETAN = self.THETAN
if MAT_FLAG == 0: # element
descriptor = DESCRIPTOR
density = xraylib.ElementDensity(xraylib.SymbolToAtomicNumber(DESCRIPTOR))
elif MAT_FLAG == 1: # formula
descriptor = DESCRIPTOR
if GRID == 0: # standard energy grid
energy = numpy.arange(0,500)
elefactor = numpy.log10(10000.0 / 30.0) / 300.0
energy = 10.0 * 10**(energy * elefactor)
elif GRID == 1: # user energy grid
if GRIDN == 1:
energy = numpy.array([GRIDSTART])
else:
energy = numpy.linspace(GRIDSTART,GRIDEND,GRIDN)
elif GRID == 2: # single energy point
energy = numpy.array([GRIDSTART])
if THETAGRID == 0:
theta = numpy.array([THETA1])
else:
theta = numpy.linspace(THETA1,THETA2,THETAN)
CALCULATE_items=['f1', 'f2', 'delta', 'beta', 'mu [cm^-1]', 'mu [cm^2/g]', 'Cross Section [barn]', 'reflectivity-s', 'reflectivity-p', 'reflectivity-unpol', 'delta/beta ']
out = numpy.zeros((energy.size,theta.size))
for i,itheta in enumerate(theta):
if MAT_FLAG == 0: # element
tmp = f1f2_calc(descriptor,energy,1e-3*itheta,F=1+CALCULATE,rough=ROUGH,density=density)
out[:,i] = tmp
else:
tmp = f1f2_calc_mix(descriptor,energy,1e-3*itheta,F=1+CALCULATE,rough=ROUGH,density=density)
out[:,i] = tmp
if ((energy.size == 1) and (theta.size == 1)):
info = "** Single value calculation E=%g eV, theta=%g mrad, Result(F=%d)=%g "%(energy[0],theta[0],1+CALCULATE,out[0,0])
labels = ["Energy [eV]",CALCULATE_items[CALCULATE]]
tmp = numpy.vstack((energy,out[:,0]))
print(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>",energy.shape,out.shape,tmp.shape)
out_dict = {"application":"xoppy","name":"xf12","info":info, "data":tmp,"labels":labels}
elif theta.size == 1:
tmp = numpy.vstack((energy,out[:,0]))
labels = ["Energy [eV]",CALCULATE_items[CALCULATE]]
out_dict = {"application":"xoppy","name":"xf12","data":tmp,"labels":labels}
elif energy.size == 1:
tmp = numpy.vstack((theta,out[0,:]))
labels = ["Theta [mrad]",CALCULATE_items[CALCULATE]]
out_dict = {"application":"xoppy","name":"xf12","data":tmp,"labels":labels}
else:
labels = [r"energy[eV]",r"theta [mrad]"]
out_dict = {"application":"xoppy","name":"xf12","data2D":out,"dataX":energy,"dataY":theta,"labels":labels}
#
#
#
if "info" in out_dict.keys():
print(out_dict["info"])
#send exchange
calculated_data = DataExchangeObject("XOPPY", self.get_data_exchange_widget_name())
try:
calculated_data.add_content("xoppy_data", out_dict["data"].T)
calculated_data.add_content("plot_x_col", 0)
calculated_data.add_content("plot_y_col", -1)
except:
pass
try:
calculated_data.add_content("labels", out_dict["labels"])
except:
pass
try:
calculated_data.add_content("info", out_dict["info"])
except:
pass
try:
calculated_data.add_content("data2D", out_dict["data2D"])
calculated_data.add_content("dataX", out_dict["dataX"])
calculated_data.add_content("dataY", out_dict["dataY"])
except:
pass
return calculated_data
ytitle="Ray deviation [m]")
#
# Reflectivity
#
from orangecontrib.xoppy.util.xoppy_xraylib_util import f1f2_calc
reflectivity = energies * 0.0
for i, energy in enumerate(energies):
a = f1f2_calc(
"Au",
energy,
theta=numpy.pi / 2 - Alpha[i],
F=8,
density=None,
rough=0.0,
)
reflectivity[i] = a
# print(">>",energy,90.0-Alpha[i]*180.0/numpy.pi,a)
if do_plot:
plot(energies,
reflectivity,
yrange=[0, 1],
xtitle="Photon energy [eV]",
ytitle="Reflectivity(Pi-Alpha(E))")
#
# resolving power
